odgi flip: avoid introducing useless edges and losing edges from the original graph
#485
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Thanks for this, @AndreaGuarracino! I can recreate the fact that it now (correctly) does nothing for the graph When I run flip on note5, the only meaningful change is that If I understand |
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anshumanmohan
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Apr 18, 2023
We agree with odgi on all the handmade files except note5.gfa I think odgi is doing something fishy there; see pangenome/odgi#485 (comment) We agree with odgi on all the handmade files except flip4.gfa flip4 is not a valid graph and so arguably it does not matter what we do with it, but `odgi flip` does currently _fix_ flip4, so I think it's worth keeping around. The point of divergence is that we do not currently fix graphs like flip4, though it's easy enough to do if that were desired. See pangenome/odgi#496
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This PR introduces a different way to construct the flipped graph:
In the first tests, this avoids introducing edges that are not used in the flipped paths and avoids losing edges that are present in the input graph.